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Indonesian Journal of Biotechnology

ijbiotech
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Published by Universitas Gadjah Mada

ISSN : 08538654 EISSN : 20892241 DOI : -

Core Subject : Science,

Biochemistry, Genetics & Molecular Biology Immunology & microbiology Materials Science & Nanotechnology

The Indonesian Journal of Biotechnology (IJBiotech) is an open access, peer-reviewed, multidisciplinary journal dedicated to the publication of novel research in all aspects of biotechnology, with particular attention paid to the exploration and development of natural products derived from tropical—and especially Indonesian—biodiversity. IJBiotech is published biannually and accepts original research articles featuring well-designed studies with clearly analyzed and logically interpreted results. A strong preference is given to research that has the potential to make significant contributions to both the field of biotechnology and society in general.

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Articles 523 Documents

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Antifungal Production of a Strain of Actinomycetes spp Isolated from the Rhizosphere of Cajuput Plant: Selection and Detection of Exhibiting Activity Against Tested Fungi A. Alimuddin; Jaka Widada; Widya Asmara; M. Mustofa
Indonesian Journal of Biotechnology Vol 16, No 1 (2011)
Publisher : Universitas Gadjah Mada

Actinomycetes are bacteria known to constitute a large part of the rhizosphere microbiota. Their isolation is an important step for screening of new bioactive compounds. Culturable actinomycetes populations from cajuput plant rhizosphere soils in Wanagama I Forest UGM Yogyakarta were collected to study about their antifungal activity. Among 17 of a total 43 isolates that showed activity were screened for producing antifungi substances. Screening for antifungal activity of isolates were performed with dual culture bioassay in vitro. One isolate that was designated as Streptomyces sp.GMR-22 was the strongest against all tested fungi and appeared promising for a sources of antifungal. Culture’s supernatant and mycelia were extracted with chloroform, ethyl acetate and methanol, respectively. Antifungal activity of crude extracts was tested by diffusion method against tested fungi. The result indicates that isolates of actinomycetes from cajuput plant rhizosphere could be an interesting sources of antifungal bioactive substances.

Generation of recombinant scFv antibody against Ochratoxin A (OTA) Ranya Pranomphon; Witsanu Srila; Montarop Yamabhai
Indonesian Journal of Biotechnology Vol 22, No 2 (2017)
Publisher : Universitas Gadjah Mada

Ochratoxin A (OTA) is a mycotoxin commonly found in agricultural products and can accumulate in the blood and tissues after that consuming contaminated food. Recombinant single-chain antibody fragments (scFv) against OTA were selected from phage display libraries. After of one round of biopanning against BSA-conjugated OTA (OTA-BSA), 52 and 6 phage clones displaying scFv antibodies were isolated from human (Yamo I.3) and rabbit (Bozmix I.2) libraries. Two phage clones (one from each libraries, i.e., yOTA1e3 and bOTA2a9) showed binding to free toxin by competitive ELISA. The soluble scFv antibodies were produced by superinfecting phage clones into E. coli suppressor strain HB2151. The scFv genes from these two phage clones were sub-cloned into pKP300ΔIII vectors to generate scFv-AP fusions. The binding affinity (IC50) of antibody derived from human library was higher than those from rabbit library. The binding property of recombinant antibody in the form of scFv-AP was better than those of soluble scFv form. Cross-reactivity analysis indicated that the two recombinant antibodies did not cross-react with other soluble toxins, namely AFB1, DON, ZEN and FB. The ability to use the recombinant scFv-AP to detect contaminated toxins in agricultural product (corn) was demonstrated.

Functional Analysis of OsKANADI1, A Florigen Hd3a Interacting Protein in Rice (Oryza sativa L.) Yekti Asih Purwestri; Yuka Ogaki; Hiroyuki Tsuji; Ko Shimamoto
Indonesian Journal of Biotechnology Vol 17, No 2 (2012)
Publisher : Universitas Gadjah Mada

OsKANADI1 is considered as a florigen Hd3a interacting protein. To study the function of OsKANADI1, the expression pattern of OsKANADI1 was performed by semiquantitative RT-PCR with various wild-type tissues in the floral transition stage. The results demonstrated that OsKANADI1 was expressed in all organs of wild-type plants, but was highest in roots and leaves. We hypothesize that OsKANADI1 is a transcription factor in rice because it contains a GARP domain and posses a nuclear localization signal. To determine whether OsKANADI1 encodes a nuclear protein, full-length OsKANADI1 fused to GFP was introduced into onion epidermis cells by particle bombardment. The result revealed that OsKANADI1 was localized in the nucleus, suggesting that OsKANADI1 may be a transcription factor. Functional analysis was carried out using a reverse genetics approach to generate gain of function mutant (overexpression) and knockdown mutant (RNAi). The results showed that suppression of OsKANADI1 by RNAi displayed branching and increasing tiller number in several lines. This phenotype resembles to the Hd3a overexpressed plants indicating they possibly function in similar pathway.Key words : OsKANADI1, Transcription factor, Hd3a interacting protein, Rice

Genetic Variation of Apolipoprotein E (ApoE) in Surabaya, Palu and Alor Populations of Indonesia Pramudji Hastuti; Abdul Salam Mudzakir Sofro; Ahmad Husain Asdie; Ahmad Hamim Sadewa
Indonesian Journal of Biotechnology Vol 16, No 2 (2011)
Publisher : Universitas Gadjah Mada

Apolipoprotein E (ApoE) has been considered to play an important role in cardiovascular disorders.Several studies reported that genetic variation in ApoE locus influence plasma lipoprotein level. The objectivesof this study was to compare the frequency of ApoE genotypes and alleles in some populations of Indonesia.One hundred and ninety five voluntarily unrelated apparently healthy individuals were recruited fromSurabaya, Palu and Alor representing the western, middle and eastern populations of Indonesia, respectively.Blood samples were collected from each subject for DNA extraction. The common allelic variants of ApoE werescreened using polymerase chain reaction (PCR) and restriction fragment length polymorphism. Three allelesi.e. ε2, ε3 and ε4 were identified and five genotypes i.e. ApoE ε2/ε2, ApoE ε2/ε3, ApoE ε3/ε3, ApoE ε2/ε4, ApoE ε3/ε4 were found in three populations studied, while ApoE ε4/ε4 was absent in Surabaya, representing the westernpopulations of Indonesia. The frequency of ε2, ε3 and ε4 alleles in the western population were 0.208, 0.701and 0.092 respectively; in the middle population were 0.242, 0.618 and 0.140 respectively and in the easternpopulation of Indonesia were 0.267, 0.466 and 0.267 respectively. The highest frequency of ε2 and ε4 allelewas found in the eastern population of Indonesia. The distribution of ε2 allele were not significantly differentamong all Indonesian populations, but significantly different were found in ε3 and ε4 allele in the easternpopulation compared to those in the western and middle populations of Indonesian. It can be concluded thatthe frequency of three ApoE alleles in the western and middle populations of Indonesia was not significantlydifferent however, significantly different was observed in the frequency of ApoE ε3 and ε4 alleles from theeastern compared to those in the western and middle populations of Indonesia.

16s rRNA Sequence Analysis and Ammonium Excretion Ability of Nitrogen Fixing Bacteria Isolated from Mineral Acid Soil H. Hartono; Jaka Widada; Siti Kabirun
Indonesian Journal of Biotechnology Vol 14, No 2 (2009)
Publisher : Universitas Gadjah Mada

Nitrogen fixing bacteria defined as bacteria which is capable to transform free nitrogen molecules into ammonium v (PCR). Nitrogenase activity of these selected isolates was measured using Acetylene Reduction Assay (ARA). The ability of these selected isolates in ammonium excretion was qualitatively and quantitavely measured using Nessler reagent and spectrophotometry method respectively. Taxonomic position of the selected bacteria were determined based on their 16S rRNA sequence analysis. Genetic diversity analysis of these 15 isolates of nitrogen fixing bacteria yield eight selected bacteria for subsequent analysis. Sequence of nifH gene from all of these selected bacteria were successfully amplified. Nitrogenase assay of these selected bacteria revealed 6 isolates with high nitrogen fixation capasity namely GMA3, GMA5, GMA6, GMA9, GMA12 AND GMA 13.</div><div>Ammonium excretion analysis revealed 4 isolates which have remarkable ability of producing high level of ammonium namely GMA1, GMA3, GMA6, and GMA9. The 16S rRNA sequence analysis shown that isolates GMA3, GMA5, GMA11 and GMA12 had a close relationship with Brevibacillus formosus strain DSM 9885T, Flexibacter canadensis strain ISSDS-428, Rhizobium tropici strain rif 200849, and Azotobacter tropicalis strain RBS. Respectively, isolate GMA1 and GMA13 had a close relationship with Sthenotropphomonas sp. Strain MFC-C, while isolate GMA6 and GMA9 had a close relationship to Azotobacter vinelandii strain ISSDS-428.</div>', 'string'),(105, 'en_US', 'subject', 'nitrogen fixing bacteria, ammonium excretion, identification', 'string'),(105, 'en_US', 'sponsor', '', 'string'),(107, 'en_US', 'title', 'Effect of Probiotic Lactobacillus sp. Dad13 on Humoral Immune Response of Balb/C Mice Infected with Salmonella typhimurium', 'string'),(107, 'en_US', 'abstract', 'An indigenous strain of lactic acid bacterium (LAB) identified as Lactobacillus spp. Dad13 (Dad13), isolated from traditional fermented buffalo milk, was found to be potential as probiotic. The aim of this research was to study the effect of probiotic Dad13 on humoral immune response of Balb/C mice infected with Salmonella typhimurium. Thespecific objective was to find out the effect of different Dad13 consumption time (before and along with infection of S. typhimurium) on the humoral immune response of Balb/C mice. The experiment was conducted by in vivo trial on 20 males of Balb/C mice, age of 6-8 weeks, fed with AIN-93 standard diet. The mice were assigned into 4 groups. Each group received the following treatments, ie. Dad13 only, Dad13 before infection, Dad13 along with infection and Salmonella infection only. A volume of 100 μl Dad13 cell suspensions (1010 CFU/ml) were given by oral forced feeding daily for a week, at week 3 for group before infection and at week 4 for group of Dad13 only and Dad13 along with infection. Salmonella infection (109 CFU/ml) was given once orally at week 4 to all groups except group treated with Dad13 only. The humoral immune response of Balb/C mice was detected 2 weeks after infection by measuring the titers of IgG and IgA specific from serum and mucosal intestinal liquid samples using Enzyme-linked Immunosorbent Assay (ELISA) method. The result indicated that humoral immune response of Balb/C mice consuming Dad13 before and along with Salmonella infection were significantly different (p<0.05). Dad13 consumption along with Salmonella infection increased circulated IgG and IgA as well as secretory IgA. It can be concluded that Dad13 probiotic feeding along with infection increased humoral immune response more significantly compared to that before infection.

Bioactivity and genetic screening of marine actinobacteria associated with red algae Gelidiella acerosa Maria Ulfah; Noer Kasanah; Niken Satiti Nur Handayani
Indonesian Journal of Biotechnology Vol 22, No 1 (2017)
Publisher : Universitas Gadjah Mada

Bacterial resistance to existing antibiotics has driven a search for new antibiotics from marine actinobacteria. Bioactivity and genetic screening of actinobacteria associated with red algae Gelidiella acerosa were conducted to discover new antibacterial compounds against Vibrio alginolyticus. A total of 14 actinobacteria isolates were obtained from G. acerosa. The isolates were subjected to genetic screening for nrps (non-ribosomal peptide synthetase) and FADH2-dependent halogenase genes. The isolates’ ability to produce secondary metabolites was examined by fermentation in various media in a six-well mini plate. The bioactivity of the secondary metabolites was screened using a microtiter assay and the agar overlay method. The results showed that all 14 isolates had the nrps gene, whereas none had the halogenase gene. Meanwhile, eight of the actinobacteria isolates showed antibacterial activity against V. alginolyticus.

Cytotoxicity of Buah Merah (Pandanus conoideus Lamk.) Extract on Breast Cancer Cell Line (T47D) Tri R. Nuringtyas; Yoga Pratama; G. Galih; Subagus Wahyuono; Sukarti Moeljopawiro
Indonesian Journal of Biotechnology Vol 19, No 1 (2014)
Publisher : Universitas Gadjah Mada

Buah Merah (Pandanus conoideus Lamk.) has been extensively used to treat various diseases includingcancer. There are many varieties of buah merah and there was no scientifi c study comparing cytotoxicity ofdifferent varieties. The objective of this study was to investigate the cytotoxicity of three varieties of buah merahknown as Barugum, Maler and Yanggiru on breast cancer cell line (T47D). All samples were collected fromPapua, Indonesia. Each sample was extracted consecutively using three solvents chloroform, methanol andwater resulted to nine crude extracts. The cytotoxic activities were determined using MTT assay. The crudeextract showed the lowest IC50 was selected for further bioassay-guided fractionation. Fractionation was doneusing vacuum liquid chromatography coupled with preparative TLC to fi nd the active compounds. Severaldetection reagents were applied to TLC for identifi cation of the class of the potent compounds. The resultshowed that the potent extracts was obtained from Barugum methanol extract followed by Maler chloroformextract with IC50 value of 132.83 μg/ml and 139.72 μg/ml, respectively. All Yanggiru extracts did not showactivity. The bioassay-guided fractionation of Barugum and Maler extracts showed that the most potent fractioneluted by a mixture of hexane:ethyl acetate (75:25), was in Maler variety with IC50 value of 25,7 μg/ml, fourtimes higher than the most potent fraction of Barugum with IC50 value of 104,61 μg/ml. TLC analysis of themost potent fraction showed that the active compounds was class of terpene. Result of this study supportedthe utilization of buah merah Maler variety for breast cancer treatment.

Gynura procumbens Prevents Chemoresistance through Inhibition MDR1 Expression on MCF-7 Breast Cancer Cell Line and Sensitizes the Cells to Doxorubicin Nunuk Aries Nurulita; Edy Meiyanto; Eishou Matsuda; Masashi Kawaichi
Indonesian Journal of Biotechnology Vol 17, No 1 (2012)
Publisher : Universitas Gadjah Mada

The long-term exposure of doxorubicin (Dox) causes enhancement in MDR1 expression that leads tobreast cancer cell resistance. This protein become a serious problem in cancer treatment and also well-knownas negative prognostic factor in breast cancer malignancies. The new approach using natural chemopreventivesubstance was developed to inhibit this resistance progress. This study was aimed to investigate whether ethylacetate fraction of Gynura procumnens (FEG) can prevent chemoresistance through suppressing the MDR1 proteinexpression. MCF-7 cell was used as chemoresistance cell model. The MCF-7 cells were maintained with 100nM Dox-contained medium for five weeks. The chemoprevention effect of FEG was investigated by treatedMCF-7/Dox with sub-toxic concentration of FEG. The cytotoxic properties of MCF-7 cells were determinedusing MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide) assay. Immunofluorescenceand western blotting analysis was performed to detect the MDR1 expression. MCF-7/Dox cells need higherconcentration for inhibiting cell growth, were compared with MCF-7, shown by IC50value. The MDR1 proteinlevel elevated after Dox exposure in time dependent manner. The FEG treatment decreased MDR-1 proteinlevel with dose dependent manner. FEG in combination with DOX potentiates the DOX effect on breast cancercell growth inhibition. The FEG prevents the chemoresistance development in breast cancer cell line, MCF-7induced by Dox through inhibiting MDR1 expression. The additional of FEG enhances Dox effect on cell deathinduction. Thus, FEG could be developed as co-chemotherapy agent for reverse multidrug resistance

Succession of Actinomycetes During Composting Proccess of Dairy-Farm Waste Investigated by Culture-Dependent and Independent Approaches Mukhlissul Faatih; Jaka Widada; N. Ngadiman
Indonesian Journal of Biotechnology Vol 13, No 2 (2008)
Publisher : Universitas Gadjah Mada

Mesophilic, thermophilic, and maturation phases were recognized in composting proccess. Temperaturechanges influence the microbial communities in compost within composting proccess. Actinomycetes account for alarger part of compost microbial population. The aim of this research was to study succession of actinomycetescommunity during composting of dairy-farm waste investigated by culture-dependent and independentapproaches.In culture-independent method, the succession of actinomycetes community was analyzed by nestedpolymerasechain reaction of ribosomal intergenic spacer (nested-PCR RISA) using spesific primer F243 and primerR23S followed by a second PCR using primers F968 and R23S. In culture-dependent method actinomycetes fromcompost were isolated on selective media, starch-nitrate medium and humic-acid + vitamins medium. DNA ofactinomycetes was extracted and amplified by repetitive sequence-based PCR (rep-PCR) using primer BOXA1R. Thebanding patterns were used to generate dendrograms by UPGMA clustering with NTSYS program. Microcosmcontaining sterile rice-straw and water which is inoculated with each actinomycetes isolates was used for examiningthe ability of each isolate in rice-straw degradation.The experiment results showed that succession of both bacteria and actinomycetes was occured withincomposting proccess of dairy-farm waste. Analysed by culture-independent method revealed that the highestcommunity of compost’s bacteria was on mesophilic, thermophilic, and maturation phases, respectively. WhereasPCR-nested RISA resulted the highest population of actinomycetes was on thermophilic, maturation, and mesophilicphases, respectively. By culture-dependent method was obtained 29 actinomycetes isolates from mesophilic phase,23 isolates from thermophilic phase, and 19 isolates from maturation phase. Genetic diversity analysis of the obtainedisolates showed the presence of phylogenetic grouping on each phase of composting proccess. This result illustratedthe occurance of succession of actinomycetes community in compost. The ability of each isolates in rice-strawdegradation was different, and SnT9 isolate was found to be a promising rice-straw degrader.Keywords: succession, actinomycetes, composting, nested-PCR RISA, rep-PCR

Determination of allelopathic potential in mahogany (Swietenia macrophylla King) leaf litter using sandwich method Arnia Sari Mukaromah; Yekti Asih Purwestri; Yoshiharu Fujii
Indonesian Journal of Biotechnology Vol 21, No 2 (2016)
Publisher : Universitas Gadjah Mada

The sandwich method is a reliable screening bioassay that can be utilized to investigate allelopathic activity of leaf litter leachates. Screening the allelopathic potential of mahogany (Swietenia macrophylla King) leaf litter in plant–plant interaction using the sandwich bioassay method has not been reported. The research objectives were to determine and categorize allelopathic potential of S. macrophylla leaf litter using the sandwich bioassay method, and to determine specific activity (EC550). S. macrophylla leaf litter. The results showed that S. macrophylla leaf litter exhibited strong allelopathic activity when compared with 46 leaf litter species and was included in the top ten of allelopathic leaf litter species. Increasing S. macrophylla leaf litter concentration was concomitant with inhibition of radicle lettuce seedling growth compared with the control. According to the linear regression analysis, the effective concentration (EC50) of S. macrophylla was estimated to be 3.25 mg D.W. eq. mL-1 and was considered to have strong growth-inhibitory activity on lettuce radicle elongation. The results suggest the possibility of allelopathic potential of leaf litter in plant–plant interaction under S. macrophylla trees.

Page 20 of 53 | Total Record : 523

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